This script is used for predicting subclone purity.
Get Dependent data
Get the version of genome fasta that you mapped your fastqs, we support hg18 and hg19 genome fasta now.
## use built-in script
cd methylpurify/db
bash genome.sh hg18Get Dependent software
If your system is debian-like system, try:
sudo apt-get install python-numpy
sudo apt-get install samtoolsEasy to start
Input: BAM file, this should be mapped with BSMap with -R option * BSMap
Currently, we only support hg19 and hg18 genome index mapped BAM file.
If your fastq mapping is done with hg19 index, use following command:
MethylPurify -f input.bam -b 300 -c 20 -s 50 --species hg19 -g /path/to/hg19.faOptions
-f: input BAM file
-c: coverage level
-b: genome bin size
-s: sampling times
–species: species genome version
-g: species genome fasta file(correspond to –species)
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